The code/ folder has various different scripts for previous model curations that are not that intuitive to reuse. Instead, it would be beneficial to have a function that can perform various model curations, plus a standardized text file format where the necessary data is kept.
Introduced in #300, code/curateMetsRxnsGenes() can do exactly that. Standardized TSV files, exemplified for a few reactions in sulfur metabolism, can be prepared for either (a) addition of new reactions, metabolites and/or genes; or (b) editing the annotation of existing reactions, metabolites and/or genes.
For future usage, one can simply take the TSV files as templates and modify for the particular curations that should be done, runcurateMetsRxnsGenes() and get the updated model.
While the function does numerous checks for finding duplicate reactions etc., and the function can be used in various ways, it is not intended as covering all types of curations. However, it is at least a standardized way that should hopefully simplify future addition and editing of reactions, metabolites and genes. The function will likely move into the RAVEN toolbox, but is for now kept on the yeast-GEM repo.
Description of the issue:
The
code/folder has various different scripts for previous model curations that are not that intuitive to reuse. Instead, it would be beneficial to have a function that can perform various model curations, plus a standardized text file format where the necessary data is kept.Introduced in #300,
code/curateMetsRxnsGenes()can do exactly that. Standardized TSV files, exemplified for a few reactions in sulfur metabolism, can be prepared for either (a) addition of new reactions, metabolites and/or genes; or (b) editing the annotation of existing reactions, metabolites and/or genes.For future usage, one can simply take the TSV files as templates and modify for the particular curations that should be done, run
curateMetsRxnsGenes()and get the updated model.While the function does numerous checks for finding duplicate reactions etc., and the function can be used in various ways, it is not intended as covering all types of curations. However, it is at least a standardized way that should hopefully simplify future addition and editing of reactions, metabolites and genes. The function will likely move into the RAVEN toolbox, but is for now kept on the yeast-GEM repo.
I hereby confirm that I have:
mainbranch of the repository